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For: Sale K, Faulon JL, Gray GA, Schoeniger JS, Young MM. Optimal bundling of transmembrane helices using sparse distance constraints. Protein Sci 2004;13:2613-27. [PMID: 15340162 PMCID: PMC2286557 DOI: 10.1110/ps.04781504] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Revised: 06/23/2004] [Accepted: 06/23/2004] [Indexed: 10/26/2022]
Number Cited by Other Article(s)
1
Sun S, Wu X, Hu B, Guo M, Zhao X, Wang J. High voltage pulsed electric field: A novel method for killing parasitic eggs on the surface of raisins. Food Res Int 2024;196:115127. [PMID: 39614586 DOI: 10.1016/j.foodres.2024.115127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 09/05/2024] [Accepted: 09/20/2024] [Indexed: 12/01/2024]
2
Del Alamo D, Tessmer MH, Stein RA, Feix JB, Mchaourab HS, Meiler J. Rapid Simulation of Unprocessed DEER Decay Data for Protein Fold Prediction. Biophys J 2020;118:366-375. [PMID: 31892409 PMCID: PMC6976798 DOI: 10.1016/j.bpj.2019.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/13/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023]  Open
3
Jeschke G. Characterization of Protein Conformational Changes with Sparse Spin-Label Distance Constraints. J Chem Theory Comput 2012;8:3854-63. [PMID: 26593026 DOI: 10.1021/ct300113z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
4
Ueno Y, Kawasaki K, Saito O, Arai M, Suwa M. Folding elastic transmembrane helices to fit in a low-resolution image by electron microscopy. J Bioinform Comput Biol 2011;9 Suppl 1:37-50. [PMID: 22144252 DOI: 10.1142/s0219720011005720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/02/2011] [Accepted: 09/15/2011] [Indexed: 11/18/2022]
5
Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011;111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
6
A photon-free approach to transmembrane protein structure determination. J Mol Biol 2011;414:596-610. [PMID: 22024595 DOI: 10.1016/j.jmb.2011.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 10/04/2011] [Accepted: 10/11/2011] [Indexed: 02/05/2023]
7
Jha AN, Vishveshwara S, Banavar JR. Amino acid interaction preferences in helical membrane proteins. Protein Eng Des Sel 2011;24:579-88. [PMID: 21666247 DOI: 10.1093/protein/gzr022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
8
Nikiforovich GV, Marshall GR, Baranski TJ. Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor. Proteins 2010;79:787-802. [PMID: 21287612 DOI: 10.1002/prot.22918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 11/07/2022]
9
Fabris D, Yu ET. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. JOURNAL OF MASS SPECTROMETRY : JMS 2010;45:841-60. [PMID: 20648672 PMCID: PMC3432860 DOI: 10.1002/jms.1762] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
10
Yeagle PL, Albert AD. Membrane protein fragments reveal both secondary and tertiary structure of membrane proteins. Methods Mol Biol 2010;654:283-301. [PMID: 20665272 DOI: 10.1007/978-1-60761-762-4_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
11
Pan Y, Konermann L. Membrane protein structural insights from chemical labeling and mass spectrometry. Analyst 2010;135:1191-200. [DOI: 10.1039/b924805f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
12
Harrington SE, Ben-Tal N. Structural Determinants of Transmembrane Helical Proteins. Structure 2009;17:1092-103. [DOI: 10.1016/j.str.2009.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 12/16/2022]
13
Alpha-helical topology prediction and generation of distance restraints in membrane proteins. Biophys J 2008;95:5281-95. [PMID: 18775963 DOI: 10.1529/biophysj.108.132241] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
14
Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data. Biophys J 2008;95:5349-61. [PMID: 18676641 DOI: 10.1529/biophysj.108.142984] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
15
Wendel C, Gohlke H. Predicting transmembrane helix pair configurations with knowledge-based distance-dependent pair potentials. Proteins 2008;70:984-99. [PMID: 17847096 DOI: 10.1002/prot.21574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
16
Pabuwal V, Li Z. Network pattern of residue packing in helical membrane proteins and its application in membrane protein structure prediction. Protein Eng Des Sel 2008;21:55-64. [DOI: 10.1093/protein/gzm059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
17
Kovacs JA, Yeager M, Abagyan R. Computational prediction of atomic structures of helical membrane proteins aided by EM maps. Biophys J 2007;93:1950-9. [PMID: 17496035 PMCID: PMC1959528 DOI: 10.1529/biophysj.106.102137] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 04/27/2007] [Indexed: 11/18/2022]  Open
18
Schiemann O, Prisner TF. Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 2007;40:1-53. [PMID: 17565764 DOI: 10.1017/s003358350700460x] [Citation(s) in RCA: 428] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
19
Bhatnagar J, Freed JH, Crane BR. Rigid body refinement of protein complexes with long-range distance restraints from pulsed dipolar ESR. Methods Enzymol 2007;423:117-33. [PMID: 17609128 DOI: 10.1016/s0076-6879(07)23004-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
20
Yeagle PL, Albert AD. G-protein coupled receptor structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006;1768:808-24. [PMID: 17097603 DOI: 10.1016/j.bbamem.2006.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 10/02/2006] [Accepted: 10/05/2006] [Indexed: 11/18/2022]
21
Park Y, Helms V. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns. Proteins 2006;64:895-905. [PMID: 16807902 DOI: 10.1002/prot.21025] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
22
Fleishman SJ, Ben-Tal N. Progress in structure prediction of α-helical membrane proteins. Curr Opin Struct Biol 2006;16:496-504. [PMID: 16822664 DOI: 10.1016/j.sbi.2006.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Revised: 06/05/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
23
Zhang Y, DeVries ME, Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput Biol 2006;2:e13. [PMID: 16485037 PMCID: PMC1364505 DOI: 10.1371/journal.pcbi.0020013] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Accepted: 01/11/2005] [Indexed: 12/22/2022]  Open
24
Bowie JU. Solving the membrane protein folding problem. Nature 2005;438:581-9. [PMID: 16319877 DOI: 10.1038/nature04395] [Citation(s) in RCA: 354] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
25
Fanelli F, De Benedetti PG. Computational Modeling Approaches to Structure−Function Analysis of G Protein-Coupled Receptors. Chem Rev 2005;105:3297-351. [PMID: 16159154 DOI: 10.1021/cr000095n] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
26
Brown WM, Faulon JL, Sale K. A deterministic algorithm for constrained enumeration of transmembrane protein folds. Comput Biol Chem 2005;29:143-50. [PMID: 15833442 DOI: 10.1016/j.compbiolchem.2005.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/28/2004] [Accepted: 11/01/2004] [Indexed: 11/30/2022]
27
van Dijk ADJ, Boelens R, Bonvin AMJJ. Data-driven docking for the study of biomolecular complexes. FEBS J 2004;272:293-312. [PMID: 15654870 DOI: 10.1111/j.1742-4658.2004.04473.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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